vdW_grid_bench

Van der Waals 3D grid initialization benchmark

problem statement

We want to know the interaction energy between one atom [l_a] located at any grid point [i,j,k] and a fixed set of atoms [A]. We use the Van der Waals non-bonded interaction energy and Universal Force Field (UFF) parameters.

standard OCaml; before loop modification

time ./grid_init -dx 0.1 -l data/lig.pqrs -p data/prot.pqrs real 1m19.899s

w/ dune's --profile=release

real 1m10.603s

w/ V3 @@inline annotations plus dist2 optims

real 0m57.384s

w/ optims in vdW_grid

real 0m49.096s

w/ pow3 and V3.dist2 instead of pow6 and V3.dist in vdW_grid

real 0m41.282s